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{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX7967674"} | 10-cell pool-and-split control breast biopsy sample from a Stage 1 Grade 2 breast tumor (UVABC1) replicate 18, with no treatment. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX7967674"} | Endometrium tissue sample from a fertile, healthy female donor during day 11 of the menstrual cycle. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX7967674"} | A paediatric pro B-cell line derived from acute lymphoblastic leukemia (ALL) with t(4;11)(q21;q23) translocation, cultured as a cell line named SEM, and sequenced for nascent RNA. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX5430115"} | Primary monocytes from IgAN patients' peripheral blood. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX5430115"} | A tissue sample from a digital papillary adenocarcinoma (DPA), a type of eccrine sweat gland cancer. The sample, named VR182, is associated with ontology terms related to various types of cancers, adenocarcinomas, skin diseases, and neoplasms. The tissue has not received any treatment. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX5430115"} | PDAC_FFPE\_53 is a tissue sample from a patient with pancreatic ductal adenocarcinoma (PDAC), a type of pancreatic carcinoma that affects the endocrine system. This neoplasm is a malignant epithelial tumor localized in the pancreatic ducts, classified as an adenocarcinoma, which is a common form of cancer. The sample does not indicate any specific treatment. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX10814696"} | Human extended pluripotent stem (EPS) cells treated with PD0325901_A83-01, derived from the trophectoderm tissue. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX10814696"} | iCell Endothelials cell line treated with 184\_VHGO\_1 from the VHGO class and a dose of 1. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX10814696"} | 35-day old eNb1 stem cells. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX303841"} | A mixture of two samples, Sample A (UHRR) and Sample B (HBRR), with a ratio of 3:1, from the SEQC study. The cells were sequenced using Illumina HiSeq 2000 platform at AGR site, with library ID 1 and lane L04, barcode TTAGGC, and flowcell BD0J2JACXX. The sample type is tissue, and there is no reported treatment. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX303841"} | H9 induced pluripotent stem cells (iPSCs) at the early G1 phase of the cell cycle, treated with a control treatment. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX303841"} | 1649B is a cell line of induced pluripotent stem cells (iPSCs) derived from peripheral blood mononuclear cells (PBMCs) with a Major/Major genotype at the 1p13 locus. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX19355040"} | 21-020 is a reference tissue sample taken from the kidney cortex of a patient, sourced via nephrectomy and sequenced using SLIDE-Seq2 assay. The raw data can be found at atlas.kpmp.org with the ID 21-020-LN. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX19355040"} | The sample is a cultured cell line of HK1 with eGFP-tagged EBV, which did not receive any treatment (only DMSO). | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX19355040"} | hES-derived endocrine cells (strain Mel1, passages 15-30, cell id 797367, clone C_30, genotype HNF1A HET) at differentiation day 25, from batch A34. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX4386191"} | 12-3 strain of human dermal fibroblasts, treated with CFIm25 siRNA, harvested 48 hours after treatment. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX4386191"} | CD36lo macrophages from primary tonsil tissue of donorA. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX4386191"} | A tissue sample from the myometrium of a non-uterine fibroid patient, with wild-type (WT) med12 status, HMB status, and in the proliferative phase of the menstrual cycle, taken from Batch_1 of a study. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX8436996"} | CD45+CD3+ T cells from resected lung tumors. The study focused on lung disease, cellular proliferation, respiratory system disease, lung cancer, hematopoietic cells, neoplasm, cancer, leukocytes, lymphocytes, and disease. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX8436996"} | Primary peripheral blood morphonuclear cells unstimulated culture from a donor with high interferon-γ producing asthma. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX8436996"} | Astrocytoma cell line (CGGA\_698) with neoplastic cells. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX4681272"} | SHSY5Y-MYCN-TR neuroblastoma cells treated with Doxycyclin. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX4681272"} | Induced pluripotent stem cells (iPSCs) from a male, Caucasian donor, with the cell line named H28126. The cells are of the somatic stem cell type and are cultured. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX4681272"} | 60-year-old African American female with a mixed Candida/bacterial phenotype, 20 days relative to first time point, mRNA extracted from whole blood. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX6978330"} | 56.1 year old female with rheumatoid arthritis (RA) who did not respond to Adalimumab treatment, with PBMC (peripheral blood mononuclear cells) sample taken before treatment, with negative RF (rheumatoid factor) and positive anti-CCP (anti-cyclic citrullinated peptide) test results, and normal hemoglobin, leukocyte, and thrombocyte counts. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX6978330"} | CD4+ T cells from a healthy donor, infected with the HIV strain YU2. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX6978330"} | 42-day old, inferred iRN cells from human embryonic stem cell derived cortical neurons. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX3058626"} | 13.2 week developing kidney tissue sample from hMARIS\_SIX2+\_MEIS1+\_polyA#1 study with no treatment. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX3058626"} | Sample from a male patient (ID 8 | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX3058626"} | A sample of Foreskin Human Fibroblasts (hFib-MYOD line) that has been cultured, with 1446450 mapped fragments and no debris or clumping. The sample was taken from the prepuce of the penis, and it was not a control sample. The media used was DM, and it was replicate R2 at time point T72. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX15213320"} | 5-Aza-CdR + GSK-126 treated HepG2 cell line, which is a liver hepatocellular carcinoma with wildtype genotype, cultured cells derived from a Caucasian male individual. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX15213320"} | Cancer cell sample from a patient-derived cell culture, originating from a metastatic (nodal) tumor in the right dorsal tongue, posterior-lateral region. The tumor has invaded lymph nodes at levels 1 and 2, with a stage of pT4apN2c and grade of 2-3. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX15213320"} | 7-089-1 baseline adipose tissue sample (CID3) from individual 7-089-1. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX11362760"} | A sample of tissue from a primary melanoma tumor in a human brain, specifically slide serial number V10A21-107-D1 from a study on spatial transcriptomics of a human brain metastasis (patient 16). | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX11362760"} | Cord blood cells transduced with CBFA2T3\_GLIS2 at six weeks post-transduction. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX11362760"} | Post-mortem cortex frontal tissue from subject MSSM-JC-23, part of the Other Neurological Disorders group in the NYGC ALS Consortium study, with no reported treatment. The sample has been prepared using the Automated KAPA Total library preparation method. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX11120603"} | 3 hour control stimulation of primary male monocytes. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX11120603"} | Nasopharyngeal samples from Patient28, collected on December 21, 2016, in Manhattan, USA. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX11120603"} | iCell Neurons that have been differentiated in vitro with no treatment (MethodBlank\_0). | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX11069330"} | 28-week-old male cells of the PBMC type, taken from a site with high malaria transmission, vaccinated with rtss, and not infected with malaria at the time of sampling. The cells were taken from the subject 365 days after the initial visit (M0) and were not infected with malaria before that visit either. The subject's Waz and Haz scores were 0.36 and -1.68, respectively, and their hemoglobin level was 7.9 g/dL at the time of sampling. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX11069330"} | Malignant ascites from a patient with advanced gastric cancer (AGC04). | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX11069330"} | hPSC-derived astrocytes from the H9 line, differentiated in vitro, taken from the dorsal horn of the spinal cord. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX365217"} | 24-hour ethanol-treated MCF7 cell line derived from a Caucasian adult female breast adenocarcinoma patient. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX365217"} | ES-derived lung progenitor cells at day 15, control treatment. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX365217"} | A sample of the MDA-MB-231 breast cancer cell line bone metastatic variant (BrM2), which is a mammary gland/breast epithelial cell line, cultured in the lab. This cell line is associated with adenocarcinoma, a disease characterized by excessive cell proliferation, specifically in the mammary gland epithelial cells, and is derived from a female Caucasian adult with breast cancer that has metastasized to the bone. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX483404"} | Peripheral T-cell lymphoma not otherwise specified (PTCL-NOS) cells from a lymph node sample, with a karyotype of 38-47,XX,+X[10],+2[12],+3[2],del(6)(q15q25),+7[13],add(16)(q24)[14],-18[10],-20[9][cp16]. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX483404"} | 48 hours post-treatment with ETO 10uM, colorectal carcinoma cells (HCT116 line) were used in a DNTR-seq mRNA study. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX483404"} | 15-17 days post symptom onset, whole blood sample from a non-severe, male, 14-year-old patient. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX5668924"} | hES-derived endocrine cells (strain Mel1, passages 15-30, clone C\_13, genotype KO1, cell ID 797447) at differentiation day 25, cultured in vitro. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX5668924"} | 19-year-old female bone marrow sample from a untreated individual with SAA condition, characterized by surface markers Lin-CD34+. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX5668924"} | K562 cells, a line of chronic myelogenous leukemia cells, with a bcr:abl fusion genotype, treated with Doxorubicin and Imatininb. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX13968025"} | Induced pluripotent stem cell differentiated endothelial cells used in an in-vitro study. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX13968025"} | 529 is a breast cancer cell line (MCF-7, adenocarcinoma) treated with BPAP (Bisphenol AP) at a dose of 5, as part of Plate 2C index E, pool 2, in a study of cellular proliferation diseases. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX13968025"} | HEK293 cell line sample, prepared using sci-RNA-seq, derived from kidney cells. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX746118"} | Sample con\_1 is a cell line (SW48) derived from a human colon adenocarcinoma, cultured under control conditions. It represents colorectal adenocarcinoma, a type of colon adenocarcinoma, which is a digestive system disease and a form of neoplasm (cancer) that affects cellular proliferation. This cell line is specifically classified as an epithelial neoplasm and colon carcinoma, which falls under colorectal cancer and intestinal cancer, and is associated with kidney disease. The SW48 cell line is derived from a Caucasian female organism, and it is a colonic neoplasm, which is another term for colon cancer. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX746118"} | 23-year-old female's primary blood monocyte cells, control group, with 437098 uniquely mapped reads and 1 virus read. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX746118"} | 54-day cultured embryonic stem cells that have been viral barcoded, but not treated with any specific agent. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX3798293"} | CD45+CD3+CD8+CD103plus/minus T cells from donor Donor-40, isolated from a tumor, with no reported treatment. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX3798293"} | iPSC-derived cardiac myocytes from the iPS-GM942-SeV3-CMs cell line, cultured in vitro. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX3798293"} | A sample of healthy tissue from a female donor, aged 36-74 with a mean age of 51, who received treatment with Culture/DMSO. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX1225252"} | The sample is a cell line (H208 | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX1225252"} | Primary cells from a female donor with new onset T1D, specifically Islet-reactive CD4+ T-cells, aged 34 years, with no treatment. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX1225252"} | Primary CD8 T lymphocytes from peripheral blood of melanoma patients who responded to Nivolumab treatment, collected at time point T2. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX14667290"} | K562 cells cultured under normoxia condition, which is a type of chronic myeloid leukemia (CML) cell line derived from a female patient's bone marrow. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX14667290"} | 2i-treated heart cells derived from human induced pluripotent stem cells (hiPS), infected with 4F adenovirus, and stained with Red for FUCCI. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX14667290"} | 17-year-old female patient with severe dengue, whose blood sample (containing PBMCs) consists primarily of monocytes, with 88002 uniquely mapped human reads and no virus reads. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX9862384"} | A tissue sample from a gastric cancer tumor (SUVmax=28) of a patient, with no specified treatment. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX9862384"} | 51-year-old female patient with acute promyelocytic leukemia (APL), specifically bone marrow mononuclear cells. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX9862384"} | This sample is a shRNA control cell line (U251) with passages ranging from 14-18, derived from a brain tissue of a patient with glioblastoma multiforme, a type of astrocytoma and nervous system cancer. The cell line is a part of the study focusing on diseases with cellular proliferation. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX11096050"} | B-cell precursor leukemia cell line NALM-6 treated with uninfected T-cells using SMARTseq2 library strategy. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX11096050"} | 293T kidney cells (HEK293T Cells) that have been transduced with the APOBEC1-YTH transgene and treated with 1 microgram/mL doxycycline for 24 hours. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX11096050"} | Primary cells from a blood sample, specifically gamma-delta T cells, treated with Bacillus Calmette-Guérin. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX17909128"} | A sample of non-treated whole blood from a male subject, taken 4 days after the first sample, which tested negative for SARS-CoV-2 antibodies and infection. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX17909128"} | 48-hour RNA sequencing sample of primary blood cells (PBMCs) taken from a male donor at room temperature, with no culture or biobank history, using Smart-seq2 technology. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX17909128"} | Cancer cell line (MM047) treated with siPRRX1_1 in vitro, with phenotype related to melanoma and cellular proliferation disease. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX5430482"} | 36 is a sample of adjacent normal mucosa tissue, not associated with any tumor stage, tobacco smoking, or alcohol consumption. It is referred to as ANM\_36 and has been mapped with ontology terms related to nicotine dependence and mucosa. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX5430482"} | 19-week-old fetal human liver tissue, freshly isolated. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX5430482"} | Descending colon pinch biopsy tissue from a patient with UC inactive condition. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX4356434"} | 24-year-old female's primary T cells from blood (PBMCs) with no virus reads and 3,724,806 human uniquely mapped reads, serving as a control sample. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX4356434"} | 30.8794520547945 year old female with mild disease, whose peripheral blood sample was taken at 16 weeks post-infection (16wpi) for RNA sequencing. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX4356434"} | 85-year-old male frontal cortex tissue sample with no treatment, post-mortem delay of 445 hours, and RIN value of 7.20. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX2657990"} | K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, biorep 2, batch 6 cell line derived from a female chronic myelogenous leukemia patient. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX2657990"} | HEK293 cell line samples, assayed with sci-RNA-seq, derived from kidney cells. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX2657990"} | Human tissue sample TT\_HS from source PT1\_MTT52 with no reported treatments. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX15832637"} | A sample of Lung Adenocarcinoma (A549) cells with wild-type genotype, treated with combinations of drugs at 10 uM concentration. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX15832637"} | A skin sample from donor APC76 with the condition PSO (Psoriasis). | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX15832637"} | Sample P4 consists of limb-girdle muscular dystrophy type 2 (LGMDD2) patient-derived primary blood mononuclear cells (PBMCs). | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX13266153"} | induced astrocytes from a NEDAMSS patient who received cuatsm drug treatment, represented by rep3 in the study. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX13266153"} | 75 year old male neuroendocrine cancer cells (KRJ1) treated with Lapatinib. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX13266153"} | Sample of long-term hematopoietic stem cells (LT-HSC) isolated from mobilized peripheral blood at day 3 post-treatment, specifically from donor mPB3, batch B3, with no reported treatment. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX3468230"} | Tenosynovium tissue sourced during CTS decompression surgery, with genome build GRCh38 and CTS condition. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX3468230"} | Sample NTX28214sc\_90 contains clear cell renal cell cancer cells from a patient with the same identifier. It is a cell line sample with no specified treatment. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX3468230"} | Primary oral squamous cell carcinoma (OSCC) cells, passages 13-15, resistant to cisplatin treatment. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX12298998"} | 7-day old induced pluripotent stem cells (hiPSCs) differentiated through spin embryoid body (Spin-EB) method, donor 3. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX12298998"} | A tissue sample from the retina, named P3\_Mac, with no reported treatment. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX12298998"} | Macrophages (MDMs) from an individual named D8, differentiated in vitro, treated with M-CSF protein and Atripla drug. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX13807217"} | 13.5 year old patient with sub-clinical TB or progressor follow-up, with whole blood sample showing positive mtb culture, normal chest x-ray, positive QFT result, and 7 mm induration in TST. | 1 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX13807217"} | Whole blood sample from a patient with acute brucellosis who has achieved complete remission after treatment, part of Group 1 in a study of suspected brucellosis cases in Macedonia. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX13807217"} | Primary cells from peripheral blood, specifically early pre-DC2 dendritic cells, which passed quality control checks. These cells are hematopoietic and leukocytic, and belong to the plasmacytoid dendritic cell type. | 0 |
{"file_record": {"dataset_path": "data/RNA/processed/train/geo_70k/train.h5ad", "embeddings": {"X_hvg": "data/RNA/processed/train/geo_70k/train_X_hvg_embedding.npz", "X_pca": "data/RNA/processed/train/geo_70k/train_X_pca_embedding.npz", "X_scvi": "data/RNA/processed/train/geo_70k/train_X_scvi_embedding.npz", "X_geneformer": "data/RNA/processed/train/geo_70k/train_X_geneformer_embedding.npz"}}, "sample_id": "SRX7775231"} | 38-year-old male peripheral blood sample from an untreated individual. | 1 |
Subsets and Splits